Merge pull request #151 from neuroscout/fix/download

Fix incorrect CLI flags

Dockerfile

@@ -14,11 +14,7 @@ RUN git config --global  user.email "user@example.edu"
 COPY [".", "/src/neuroscout"]
 
 RUN /bin/bash -c "source activate neuro \
-      && pip install -q --no-cache-dir -e /src/neuroscout/" \
-    && sync
-
-RUN /bin/bash -c "source activate neuro \
-      && pip install -q --no-cache-dir --upgrade -r /src/neuroscout/requirements.txt" \
+      && pip install -q --no-cache-dir /src/neuroscout/" \
     && sync
 
 WORKDIR /work

neuroscout_cli/cli.py

@@ -9,11 +9,10 @@
 import click
 import warnings
 warnings.filterwarnings("ignore", category=FutureWarning)
-import neuroscout_cli.commands as ncl
-from fitlins.cli.run import run_fitlins
 logging.getLogger().setLevel(logging.INFO)
 
 def fitlins_help(ctx, param, value):
+    from fitlins.cli.run import run_fitlins
     if not value or ctx.resilient_parsing:
         return
     run_fitlins(['--help'])
@@ -69,7 +68,8 @@ def run(**kwargs):
 
         docker run --rm -it -v /local/dir:/out neuroscout/neuroscout-cli run a54oo /out
     """
-    sys.exit(ncl.Run(kwargs).run())
+    from neuroscout_cli.commands import Run
+    sys.exit(Run(kwargs).run())
 
 
 @click.argument('out_dir', type=click.Path())
@@ -87,7 +87,8 @@ def get(**kwargs):
     
     Note: `run` automatically calls `get` prior to execution, by default.
     """
-    sys.exit(ncl.Get(kwargs).run())
+    from neuroscout_cli.commands import Get
+    sys.exit(Get(kwargs).run())
 
 @click.argument('out_dir', type=click.Path())
 @click.argument('analysis_id')
@@ -101,4 +102,5 @@ def upload(**kwargs):
    
    Note: `run` automatically calls `upload` after execution, by default.
    """
-   sys.exit(ncl.Upload(kwargs).run())
+   from neuroscout_cli.commands import Upload
+   sys.exit(Upload(kwargs).run())

neuroscout_cli/commands/base.py

@@ -12,7 +12,6 @@ class Command(metaclass=ABCMeta):
 
     def __init__(self, options):
         self.options = options
-        print(self.options)
         self.bundle_id = self.options['analysis_id']
         self.api = Neuroscout()
         self.main_dir = Path(self.options['out_dir']) / f'neuroscout-{self.bundle_id}'

neuroscout_cli/commands/get.py

@@ -20,13 +20,10 @@ class Get(Command):
 
     def __init__(self, options):
         super().__init__(options)
-        self.resources = None
-        self.download_dir = self.options.get('--download-dir', None)
+        self.download_dir = self.options['download_dir']
         if self.download_dir is not None:
             self.download_dir = Path(self.download_dir)
 
-        self.preproc_dir = None
-
         # Make dirs
         self.main_dir.mkdir(parents=True, exist_ok=True)
         self.bundle_dir.mkdir(parents=True, exist_ok=True)        
@@ -83,13 +80,11 @@ def download_bundle(self):
 
     def download_data(self):
         """ Use DataLad to download necessary data to disk """
-        self.download_bundle()
         with self.model_path.open() as f:
             model = convert_JSON(json.load(f))
 
         try:
             # Custom logic to fetch and avoid indexing dataset
-            preproc_dir = self.preproc_dir
             paths = []
 
             # Custom logic to fetch relevant files
@@ -114,14 +109,14 @@ def download_data(self):
                 for run in runs:
                     for task in tasks:
                         pre =  f'sub-{sub}/**/func/*{task}{run}space-MNI152NLin2009cAsym*'
-                        paths += list(preproc_dir.glob(pre + 'preproc*.nii.gz'))
-                        paths += list(preproc_dir.glob(pre + 'brain_mask.nii.gz'))
+                        paths += list(self.preproc_dir.glob(pre + 'preproc*.nii.gz'))
+                        paths += list(self.preproc_dir.glob(pre + 'brain_mask.nii.gz'))
 
             if not paths:
                 raise Exception("No images suitable for download.")
 
             # Get all JSON files
-            paths += list(preproc_dir.rglob('*.json'))
+            paths += list(self.preproc_dir.rglob('*.json'))
 
             # Get with DataLad
             get([str(p) for p in paths], dataset=self.preproc_dir.parent)
@@ -154,5 +149,10 @@ def _check_version(self):
             sys.exit(1)
 
     def run(self):
-        return self.download_data()
+        retcode = self.download_bundle()
+
+        if not self.options.get('bundle_only', False):
+            retcode = self.download_data()
+
+        return retcode
 

neuroscout_cli/commands/run.py

@@ -14,17 +14,17 @@ class Run(Get):
 
     def run(self):
         # Download bundle and get dataset if necessary
-        if not self.options.get('--no-get', False):
+        if not self.options['no_get']:
             retcode = super().run()
 
         # Need to retrieve this from fitlins output once it's available
         fitlins_args = [
             str(self.preproc_dir),
             str(self.main_dir),
             'dataset',
-            f'--model={self.model_path}',
+            f'--model={str(self.model_path.absolute())}',
             '--ignore=/(.*desc-confounds_regressors.*)/',
-            f'--derivatives={str(self.bundle_dir)} {str(self.preproc_dir)}',
+            f'--derivatives={str(self.bundle_dir.absolute())} {str(self.preproc_dir.absolute())}',
         ]
 
         # Append pass through options
@@ -52,7 +52,7 @@ def run(self):
                 )
             return retcode
 
-        if self.options.get('--no-upload', False):
+        if not self.options['no_upload']:
             # Upload results
             up = Upload(self.options)
             up.run(preproc_dir=self.preproc_dir)

neuroscout_cli/commands/upload.py

@@ -13,21 +13,23 @@ def __init__(self, options):
         super().__init__(options)
 
     def run(self, preproc_dir=None):
-        subject_level = self.options.get('--upload-first-level', False)
-        nv_force = self.options.get('--force-upload', False)
+        subject_level = self.options['upload_first_level']
+        nv_force = self.options['force_upload']
         resources = json.load((self.bundle_dir / 'resources.json').open())
 
         model = json.load(open(self.model_path, 'r'))
         n_subjects = len(model['Input']['Subject'])
 
-        # Load esimator from file in case of upload only
+        # Load esimator from fitlins output & neuroscout-cli options
+        saved_options = json.load(
+            (self.main_dir / 'options.json').open('r'))
         try:
-            saved_options = json.load((self.main_dir / 'options.json').open('r'))
-            estimator = saved_options.get('--estimator')
+            dataset_description = json.load(
+                (self.main_dir / 'fitlins' / 'dataset_description.json').open('r'))
+            estimator = dataset_description['PipelineDescription']['Parameters']['estimator']
         except:
             estimator = None
-            saved_options = None
-            print("No saved options found skipping...")
+            logging.info("No estimator information found skipping...")
 
         fmriprep_version = None
         if preproc_dir: